Yulia A. Bogdanova

Postgraduate (Molecular technologies laboratory)

E-mail: bogdanova.biochem@gmail.com

Selected publications

  1. Ermakova Y.G., Sen T., Bogdanova Y.A., Smirnov A.Y., Baleeva N.S., Krylov A.I., Baranov M.S. (2018). Pyridinium Analogues of Green Fluorescent Protein Chromophore: Fluorogenic Dyes With Large Solvent-Dependent Stokes Shift. J Phys Chem Lett , [+]

    Novel fluorogenic dyes based on the GFP chromophore are developed. The compounds contain a pyridinium ring instead of phenolate and feature large Stokes shifts and solvent-dependent variations in the fluorescence quantum yield, which facilitates their use for imaging the membrane structure of endoplasmic reticulum. Electronic structure calculations explain the trends in solvatochromic behavior.

  2. Ermakova Y.G., Pak V.V., Bogdanova Y.A., Kotlobay A.A., Yampolsky I.V., Shokhina A.G., Panova A.S., Marygin R.A., Staroverov D.B., Bilan D.S., Sies H., Belousov V.V. (2018). SypHer3s: a genetically encoded fluorescent ratiometric probe with enhanced brightness and an improved dynamic range. Chem. Commun. (Camb.) 54 (23), 2898–2901 [+]

    We designed a genetically encoded ratiometric fluorescent probe, SypHer3s, with enhanced brightness and optimized pK, which responds to pH changes in different cellular compartments. SypHer3s was successfully utilized for imaging the pH dynamics in mitochondria of living neurons and in quantitative pH measurement in zebrafish embryos.

  3. Bogdanova Y.A., Schultz C., Belousov V.V. (2017). Local Generation and Imaging of Hydrogen Peroxide in Living Cells. Curr Protoc Chem Biol 9 (2), 117–127 [+]

    Described here is a localized H2 O2 generation-detection system consisting of a yeast D-amino acid oxidase (DAAO) and two spectrally distinct variants of biosensor, HyPer2 and HyPerRed based on circularly permutated yellow and red fluorescent proteins, respectively, which enables spatiotemporal production and examination of the intracellular H2 O2 dynamics. The protocol describes using this system in a simple cell culture model. We provide detailed instructions on imaging of H2 O2 generated by the activated DAAO. The system can be easily optimized for various combinations of cell types, conditions and DAAO/sensor subcellular localizations. © 2017 by John Wiley & Sons, Inc.

  4. Ermakova Y.G., Lanin A.A., Fedotov I.V., Roshchin M., Kelmanson I.V., Kulik D., Bogdanova Y.A., Shokhina A.G., Bilan D.S., Staroverov D.B., Balaban P.M., Fedotov A.B., SidorovBiryukov D.A., Nikitin E.S., Zheltikov A.M., Belousov V.V. (2017). Thermogenetic neurostimulation with single-cell resolution. Nat Commun 8, 15362 [+]

    Thermogenetics is a promising innovative neurostimulation technique, which enables robust activation of neurons using thermosensitive transient receptor potential (TRP) cation channels. Broader application of this approach in neuroscience is, however, hindered by a limited variety of suitable ion channels, and by low spatial and temporal resolution of neuronal activation when TRP channels are activated by ambient temperature variations or chemical agonists. Here, we demonstrate rapid, robust and reproducible repeated activation of snake TRPA1 channels heterologously expressed in non-neuronal cells, mouse neurons and zebrafish neurons in vivo by infrared (IR) laser radiation. A fibre-optic probe that integrates a nitrogen-vacancy (NV) diamond quantum sensor with optical and microwave waveguide delivery enables thermometry with single-cell resolution, allowing neurons to be activated by exceptionally mild heating, thus preventing the damaging effects of excessive heat. The neuronal responses to the activation by IR laser radiation are fully characterized using Ca(2+) imaging and electrophysiology, providing, for the first time, a complete framework for a thermogenetic manipulation of individual neurons using IR light.

  5. Matlashov M.E., Bogdanova Y.A., Ermakova G.V., Mishina N.M., Ermakova Y.G., Nikitin E.S., Balaban P.M., Okabe S., Lukyanov S., Enikolopov G., Zaraisky A.G., Belousov V.V. (2015). Fluorescent ratiometric pH indicator SypHer2: applications in neuroscience and regenerative biology. Biochim. Biophys. Acta 1850 (11), 2318–2328 [+]


    SypHer is a genetically encoded fluorescent pH-indicator with a ratiometric readout, suitable for measuring fast intracellular pH shifts. However, a relatively low brightness of the indicator limits its use.



    Here we designed a new version of pH-sensor - SypHer-2, that has up to three times brighter fluorescence signal in cultured mammalian cells compared to the SypHer.



    Using the new indicator we registered activity-associated pH oscillations in neuronal cell culture. We observed prominent temporal neuronal cytoplasm acidification that occurs in parallel with calcium entry. Furthermore, we monitored pH in presynaptic and postsynaptic termini by targeting SypHer-2 directly to these compartments and revealed marked differences in pH dynamics between synaptic boutons and dendritic spines. Finally, we were able to reveal for the first time the intracellular pH drop which occurs within an extended region of the amputated tail of the Xenopus laevis tadpole before it begins to regenerate.



    SypHer2 is suitable for quantitative monitoring of pH in biological systems of different scales, from small cellular subcompartments to animal tissues in vivo.



    The new pH-sensor will help to investigate pH-dependent processes in both in vitro and in vivo studies.